NFM is the number of mature fruits on a tree. The levels are as follows: a: 1- 50 b: 51 - 200 c: 201 - 500 d: 501 - 1000 e: 1001 - 5000 f: 5000+
The below charts are the NFM compared with real visitation. The X axis is each “tree month” that had a camera in it. The X axis is in sequential order from earliest to latest. It has both high and low cameras.
##
## Call:
## glm(formula = real.visitation ~ NFM + Height, family = poisson,
## data = cam_data_FG)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -11.357 -6.055 -2.825 1.577 23.117
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.96847 0.05943 49.946 < 2e-16 ***
## NFMa 0.06093 0.17021 0.358 0.720
## NFMb -0.52900 0.11930 -4.434 9.24e-06 ***
## NFMc 0.58985 0.05645 10.450 < 2e-16 ***
## NFMd -0.04165 0.05732 -0.727 0.467
## NFMe 0.05648 0.05886 0.960 0.337
## Heightlow 0.60818 0.03128 19.445 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 7408.9 on 161 degrees of freedom
## Residual deviance: 6429.2 on 155 degrees of freedom
## AIC: 7125.8
##
## Number of Fisher Scoring iterations: 6
This doesnt reveal too much in the way of relationships. Lets extract trees that occur across consecutive months.
##
## Call:
## glm(formula = real.visitation ~ NFM + Height, family = poisson,
## data = conmonths)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -12.370 -5.305 -2.507 2.749 17.937
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.85294 0.26124 3.265 0.00109 **
## NFMb 1.98027 0.31250 6.337 2.35e-10 ***
## NFMc 2.72802 0.26013 10.487 < 2e-16 ***
## NFMd 1.79116 0.26081 6.868 6.53e-12 ***
## NFMe 2.23085 0.26008 8.577 < 2e-16 ***
## Heightlow 0.75650 0.03975 19.030 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for poisson family taken to be 1)
##
## Null deviance: 4499.6 on 95 degrees of freedom
## Residual deviance: 3478.9 on 90 degrees of freedom
## AIC: 3884.4
##
## Number of Fisher Scoring iterations: 6
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 4.00 19.50 34.28 41.00 237.00
## [1] 1962.388
## Best Normalizing transformation with 162 Observations
## Estimated Normality Statistics (Pearson P / df, lower => more normal):
## - No transform: 3.4747
## - Log_b(x+a): 3.6518
## - sqrt(x+a): 1.3053
## - exp(x): 5.7466
## - arcsinh(x): 1.531
## - Yeo-Johnson: 1.1246
## - orderNorm: 1.2957
## Estimation method: Out-of-sample via CV with 10 folds and 5 repeats
##
## Based off these, bestNormalize chose:
## Standardized Yeo-Johnson Transformation with 162 nonmissing obs.:
## Estimated statistics:
## - lambda = 0.1337981
## - mean (before standardization) = 3.458438
## - sd (before standardization) = 2.135431
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 + (1 + focalmonth..50 | Tree)
## Data: cam_data_FG
##
## AIC BIC logLik deviance df.resid
## 4515.4 4530.9 -2252.7 4505.4 157
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.6574 -2.8417 -0.6314 2.0048 24.2336
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.882 1.372
## focalmonth..50 1.725 1.314 -0.90
## Number of obs: 162, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.8575 0.2163 13.213 <2e-16 ***
## focalmonth..50 0.5054 0.2460 2.055 0.0399 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## fclmnth..50 -0.757
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 + (1 + focalmonth..50 | Tree) +
## (1 + focalmonth..50 | date)
## Data: cam_data_FG
##
## AIC BIC logLik deviance df.resid
## 3094.9 3119.6 -1539.4 3078.9 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.6697 -2.1365 -0.1654 1.8407 11.6675
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.7878 1.3371
## focalmonth..50 1.0429 1.0212 -0.91
## date (Intercept) 0.9082 0.9530
## focalmonth..50 0.3200 0.5657 -0.30
## Number of obs: 162, groups: Tree, 49; date, 22
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.8177 0.2923 9.641 <2e-16 ***
## focalmonth..50 0.6179 0.2570 2.404 0.0162 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## fclmnth..50 -0.523
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 + CANOPY_DENS_CENSUS_1 + ALTURA_CENSUS_1 +
## CERCROPIA_CENSUS_1 + ARB_DAP50_CENSUS_1 + (1 + focalmonth..50 |
## Tree) + (1 + focalmonth..50 | date)
## Data: cam_data_FG
##
## AIC BIC logLik deviance df.resid
## 3082 3119 -1529 3058 149
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.659 -2.155 -0.188 1.863 11.682
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.5065 1.2274
## focalmonth..50 0.9978 0.9989 -0.91
## date (Intercept) 0.9216 0.9600
## focalmonth..50 0.3294 0.5740 -0.32
## Number of obs: 161, groups: Tree, 48; date, 22
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.7505826 0.5796187 4.746 2.08e-06 ***
## focalmonth..50 0.7021152 0.2621845 2.678 0.00741 **
## CANOPY_DENS_CENSUS_1 -0.0009985 0.0113544 -0.088 0.92993
## ALTURA_CENSUS_1 0.0076531 0.0388320 0.197 0.84376
## CERCROPIA_CENSUS_1 -0.1331298 0.2088527 -0.637 0.52384
## ARB_DAP50_CENSUS_1 -0.0646910 0.2671818 -0.242 0.80868
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 CANOPY ALTURA CERCRO
## fclmnth..50 -0.344
## CANOPY_DENS -0.382 0.023
## ALTURA_CENS -0.134 0.056 -0.803
## CERCROPIA_C 0.097 -0.114 -0.252 0.040
## ARB_DAP50_C -0.024 0.086 0.069 -0.176 0.079
## convergence code: 0
## Model failed to converge with max|grad| = 0.00412225 (tol = 0.001, component 1)
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + (1 + focalmonth..50 |
## Tree) + (1 + focalmonth..50 | date)
## Data: cam_data_FG
##
## AIC BIC logLik deviance df.resid
## 2578.9 2609.8 -1279.5 2558.9 152
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -6.7081 -1.9494 -0.2202 1.2513 10.3249
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.7308 1.3156
## focalmonth..50 1.0295 1.0146 -0.86
## date (Intercept) 0.8376 0.9152
## focalmonth..50 0.3490 0.5908 -0.17
## Number of obs: 162, groups: Tree, 49; date, 22
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.12546 0.28831 7.372 1.68e-13 ***
## focalmonth..50 0.75897 0.27759 2.734 0.00625 **
## Heightlow 0.84768 0.04932 17.186 < 2e-16 ***
## focalmonth..50:Heightlow -0.07948 0.04016 -1.979 0.04779 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.438
## Heightlow -0.143 0.083
## fclmn..50:H 0.096 -0.104 -0.690
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 + (1 + focalmonth..50 | Tree) +
## (1 + focalmonth..50 | date)
## Data: binFN
##
## AIC BIC logLik deviance df.resid
## 3051.4 3076.1 -1517.7 3035.4 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.6568 -1.8778 -0.2004 1.7662 11.5114
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.9968 1.4131
## focalmonth..501 1.8719 1.3682 -0.87
## date (Intercept) 1.1793 1.0860
## focalmonth..501 0.5046 0.7104 -0.45
## Number of obs: 162, groups: Tree, 49; date, 22
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.7197 0.3258 8.348 < 2e-16 ***
## focalmonth..501 1.0187 0.3377 3.017 0.00255 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## fclmnt..501 -0.592
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 + CANOPY_DENS_CENSUS_1 + ALTURA_CENSUS_1 +
## CERCROPIA_CENSUS_1 + ARB_DAP50_CENSUS_1 + (1 + focalmonth..50 |
## Tree) + (1 + focalmonth..50 | date)
## Data: binFN
##
## AIC BIC logLik deviance df.resid
## 3038.3 3075.3 -1507.2 3014.3 149
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.6504 -1.9272 -0.1939 1.7866 11.5394
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.7281 1.3146
## focalmonth..501 1.6952 1.3020 -0.88
## date (Intercept) 1.2204 1.1047
## focalmonth..501 0.5128 0.7161 -0.46
## Number of obs: 161, groups: Tree, 48; date, 22
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.60430 0.70727 3.682 0.000231 ***
## focalmonth..501 1.09725 0.32871 3.338 0.000844 ***
## CANOPY_DENS_CENSUS_1 -0.01072 0.01289 -0.832 0.405415
## ALTURA_CENSUS_1 0.04245 0.04177 1.016 0.309506
## CERCROPIA_CENSUS_1 0.00850 0.20649 0.041 0.967167
## ARB_DAP50_CENSUS_1 -0.05709 0.25107 -0.227 0.820125
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) f..501 CANOPY ALTURA CERCRO
## fclmnt..501 -0.330
## CANOPY_DENS -0.427 0.036
## ALTURA_CENS -0.128 0.003 -0.788
## CERCROPIA_C -0.023 0.004 -0.252 0.173
## ARB_DAP50_C 0.017 0.048 -0.046 -0.048 -0.090
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + (1 + focalmonth..50 |
## Tree) + (1 + focalmonth..50 | date)
## Data: binFN
##
## AIC BIC logLik deviance df.resid
## 2536.9 2567.8 -1258.4 2516.9 152
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -6.8582 -1.9134 -0.1057 1.3413 10.0765
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.9330 1.3903
## focalmonth..501 1.8479 1.3594 -0.86
## date (Intercept) 0.9929 0.9965
## focalmonth..501 0.5051 0.7107 -0.18
## Number of obs: 162, groups: Tree, 49; date, 22
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.101854 0.312790 6.720 1.82e-11 ***
## focalmonth..501 1.145907 0.344713 3.324 0.000887 ***
## Heightlow 0.781382 0.050990 15.324 < 2e-16 ***
## focalmonth..501:Heightlow 0.001214 0.071342 0.017 0.986425
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..501 Hghtlw
## fclmnt..501 -0.513
## Heightlow -0.134 0.126
## fclm..501:H 0.096 -0.159 -0.715